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    Antibiotic resistance genes across a wide variety of metagenomes


    Fitzpatrick, David A. and Walsh, Fiona (2016) Antibiotic resistance genes across a wide variety of metagenomes. FEMS Microbiology Ecology, 92 (2). fiv168. ISSN 1574-6941

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    Abstract

    The distribution of potential clinically relevant antibiotic resistance (AR) genes across soil, water, animal, plant and human microbiomes is not well understood. We aimed to investigate if there were differences in the distribution and relative abundances of resistance genes across a variety of ecological niches. All sequence reads (human, animal, water, soil, plant and insect metagenomes) from the MG-RAST database were downloaded and assembled into a local sequence database. We show that there are many reservoirs of the basic form of resistance genes e.g. blaTEM, but the human and mammalian gut microbiomes contain the widest diversity of clinically relevant resistance genes using metagenomic analysis. The human microbiomes contained a high relative abundance of resistance genes, while the relative abundances varied greatly in the marine and soil metagenomes, when datasets with greater than one million genes were compared. While these results reflect a bias in the distribution of AR genes across the metagenomes, we note this interpretation with caution. Metagenomics analysis includes limits in terms of detection and identification of AR genes in complex and diverse microbiome population. Therefore, if we do not detect the AR gene is it in fact not there or just below the limits of our techniques?

    Item Type: Article
    Keywords: resistome; microbiome; metagenome; soil; animal; gut;
    Academic Unit: Faculty of Science and Engineering > Biology
    Item ID: 10783
    Identification Number: https://doi.org/10.1093/femsec/fiv168
    Depositing User: Fiona Walsh
    Date Deposited: 15 May 2019 14:04
    Journal or Publication Title: FEMS Microbiology Ecology
    Publisher: Oxford University Press
    Refereed: Yes
    URI:

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